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blast: init at 2.10.0 (#61430)

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Co-authored-by: Pavel Chuprikov <pschuprikov@gmail.com>
This commit is contained in:
Luis Pedro Coelho 2020-01-07 20:14:18 +01:00 committed by markuskowa
parent f8193b165f
commit fdfebafc10
3 changed files with 296 additions and 0 deletions
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108
pkgs/applications/science/biology/blast/default.nix Normal file
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@ -0,0 +1,108 @@
{ lib, stdenv, fetchurl, zlib, bzip2, perl, cpio, gawk, coreutils, ApplicationServices }:
stdenv.mkDerivation rec {
pname = "blast";
version = "2.10.0";
src = fetchurl {
url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-src.tar.gz";
sha256 = "09nry5knj5hhxpn0a5ww1gb1704grd4r1y7adbjl6kqwq37dkk9s";
};
sourceRoot = "ncbi-blast-${version}+-src/c++";
configureFlags = [
# With flat Makefile we can use all_projects in order not to build extra.
# These extra cause clang to hang on Darwin.
"--with-flat-makefile"
"--without-makefile-auto-update"
"--with-dll" # build dynamic libraries (static are default)
];
makeFlags = [ "all_projects=app/" ];
preConfigure = ''
export NCBICXX_RECONF_POLICY=warn
export PWD=$(pwd)
export HOME=$PWD
# The configure scripts wants to set AR="ar cr" unless it is already set in
# the environment. Because stdenv sets AR="ar", the result is a bad call to
# the assembler later in the process. Thus, we need to unset AR
unset AR
for awks in scripts/common/impl/is_log_interesting.awk \
scripts/common/impl/report_duplicates.awk; do
substituteInPlace $awks \
--replace /usr/bin/awk ${gawk}/bin/awk
done
for mk in src/build-system/Makefile.meta.in \
src/build-system/helpers/run_with_lock.c ; do
substituteInPlace $mk \
--replace /bin/rm ${coreutils}/bin/rm
done
for mk in src/build-system/Makefile.meta.gmake=no \
src/build-system/Makefile.meta_l \
src/build-system/Makefile.meta_r \
src/build-system/Makefile.requirements \
src/build-system/Makefile.rules_with_autodep.in; do
substituteInPlace $mk \
--replace /bin/echo ${coreutils}/bin/echo
done
for mk in src/build-system/Makefile.meta_p \
src/build-system/Makefile.rules_with_autodep.in \
src/build-system/Makefile.protobuf.in ; do
substituteInPlace $mk \
--replace /bin/mv ${coreutils}/bin/mv
done
substituteInPlace src/build-system/configure \
--replace /bin/pwd ${coreutils}/bin/pwd \
--replace /bin/ln ${coreutils}/bin/ln
substituteInPlace src/build-system/configure.ac \
--replace /bin/pwd ${coreutils}/bin/pwd \
--replace /bin/ln ${coreutils}/bin/ln
substituteInPlace src/build-system/Makefile.meta_l \
--replace /bin/date ${coreutils}/bin/date
'';
nativeBuildInputs = [ perl ];
# perl is necessary in buildInputs so that installed perl scripts get patched
# correctly
buildInputs = [ coreutils perl gawk zlib bzip2 cpio ]
++ lib.optionals stdenv.isDarwin [ ApplicationServices ];
hardeningDisable = [ "format" ];
postInstall = ''
substituteInPlace $out/bin/get_species_taxids.sh \
--replace /bin/rm ${coreutils}/bin/rm
'';
patches = [ ./no_slash_bin.patch ];
enableParallelBuilding = true;
# Many tests require either network access or locally available databases
doCheck = false;
meta = with stdenv.lib; {
description = ''Basic Local Alignment Search Tool (BLAST) finds regions of
similarity between biological sequences'';
homepage = https://blast.ncbi.nlm.nih.gov/Blast.cgi;
license = licenses.publicDomain;
# Version 2.10.0 fails on Darwin
# See https://github.com/NixOS/nixpkgs/pull/61430
platforms = platforms.linux;
maintainers = with maintainers; [ luispedro ];
};
}

184
pkgs/applications/science/biology/blast/no_slash_bin.patch Normal file
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@ -0,0 +1,184 @@
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh 2014-08-01 22:01:17.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh 2019-05-15 12:40:44.145239480 +0800
@@ -1,8 +1,5 @@
#!/bin/sh
set -e
-PATH=/bin:/usr/bin
-export PATH
-unset CDPATH
base=$1
search=`echo ${2-$LD_LIBRARY_PATH} | tr : ' '`
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh 2011-08-17 02:55:10.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh 2019-05-15 12:40:48.449276574 +0800
@@ -1,9 +1,6 @@
#!/bin/sh
id='$Id: create_flat_tuneups.sh 331412 2011-08-16 18:55:10Z ucko $'
-PATH=/bin:/usr/bin
-export PATH
-
exec > auto_flat_tuneups.mk
cat <<EOF
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh 2011-08-20 04:12:28.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh 2019-05-15 12:40:52.901315000 +0800
@@ -1,7 +1,5 @@
#!/bin/sh
-PATH=/bin:/usr/bin
-export PATH
dir=$1.lock
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh 2014-07-30 22:06:45.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh 2019-05-15 12:42:57.298410841 +0800
@@ -4,9 +4,6 @@
# Author: Denis Vakatov (vakatov@ncbi.nlm.nih.gov)
#################################
-orig_PATH=$PATH
-PATH=/bin:/usr/bin
-
script_name=`basename $0`
script_args="$*"
@@ -16,7 +13,7 @@
base_action=`basename "$action"`
case "$base_action" in
cp | cp\ * | ln | ln\ * )
- action=/bin/$base_action
+ action=$base_action
rm="rm -f"
;;
* )
@@ -58,10 +55,8 @@
shift
cmd="$* $dest_file"
test "$quiet" = yes || echo "$cmd"
- PATH=$orig_PATH
"$@" "$dest"
status=$?
- PATH=/bin:/usr/bin
return $status
}
@@ -74,7 +69,7 @@
case "$base_action" in
ln | ln\ -f )
test "$quiet" = yes || echo "failed; trying \"cp -p ...\" instead"
- cmd="/bin/cp -p $src_file $dest_file"
+ cmd="cp -p $src_file $dest_file"
ExecHelper "$dest_file" /bin/cp -p "$src_file" ||
Usage "\"$cmd\" failed"
;;
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh 2011-11-17 04:43:52.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh 2019-05-15 12:40:56.769348434 +0800
@@ -1,8 +1,6 @@
#!/bin/sh
# $Id: make_lock_map.sh 344587 2011-11-16 20:43:52Z ucko $
-PATH=/bin:/usr/bin
-export PATH
act=false
cache_dir='.#SRC-cache'
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh 2015-10-29 22:36:05.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh 2019-05-15 12:41:53.401842849 +0800
@@ -1,10 +1,6 @@
#!/bin/sh
# $Id: run_with_lock.sh 483249 2015-10-29 14:36:05Z ucko $
-orig_PATH=$PATH
-PATH=/bin:/usr/bin
-export PATH
-
base=
logfile=
map=
@@ -23,7 +19,7 @@
: ${base:=`basename "$1"`}
clean_up () {
- /bin/rm -rf "$base.lock"
+ rm -rf "$base.lock"
}
case $0 in
@@ -45,7 +41,7 @@
trap "clean_up; exit $error_status" 1 2 15
if [ -n "$logfile" ]; then
status_file=$base.lock/status
- (PATH=$orig_PATH; export PATH; "$@"; echo $? > "$status_file") 2>&1 \
+ ("$@"; echo $? > "$status_file") 2>&1 \
| tee "$logfile.new"
# Emulate egrep -q to avoid having to move from under scripts.
if [ ! -f "$logfile" ] \
@@ -58,8 +54,6 @@
status=1
fi
else
- PATH=$orig_PATH
- export PATH
"$@"
status=$?
fi
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh 2013-09-24 03:06:51.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh 2019-05-15 12:40:13.272975092 +0800
@@ -1,8 +1,5 @@
#!/bin/sh
-PATH=/bin:/usr/bin:/usr/ccs/bin
-export PATH
-
case "$1" in
--dirs )
shift
--- ncbi-blast-2.9.0+-src/scripts/common/impl/update_configurable.sh 2017-07-13 22:53:24.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/update_configurable.sh 2019-05-15 15:03:35.861276083 +0800
@@ -1,6 +1,4 @@
#!/bin/sh
-PATH=/bin:/usr/bin
-export PATH
script_name=`basename $0`
script_dir=`dirname $0`
--- ncbi-blast-2.9.0+-src/src/build-system/Makefile.mk.in 2019-01-04 01:38:37.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/src/build-system/Makefile.mk.in 2019-05-15 15:14:41.749416495 +0800
@@ -50,12 +50,12 @@
### Auxiliary commands, filters
-RM = /bin/rm -f
-RMDIR = /bin/rm -rf
-COPY = /bin/cp -p
+RM = rm -f
+RMDIR = rm -rf
+COPY = cp -p
BINCOPY = @BINCOPY@
TOUCH = @TOUCH@
-MKDIR = /bin/mkdir
+MKDIR = mkdir
BINTOUCH = $(TOUCH)
LN_S = @LN_S@
GREP = @GREP@
--- ncbi-blast-2.9.0+-src/src/build-system/configure 2019-03-05 00:49:08.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/src/build-system/configure 2019-05-15 16:55:40.711795042 +0800
@@ -10417,10 +10417,6 @@
echo "${ECHO_T}no, using $LN_S" >&6; }
fi
-case "$LN_S" in
- /*) ;;
- * ) LN_S=/bin/$LN_S ;;
-esac
if test -n "$ac_tool_prefix"; then
# Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.

4
pkgs/top-level/all-packages.nix
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@ -23673,6 +23673,10 @@ in
bftools = callPackage ../applications/science/biology/bftools { };
blast = callPackage ../applications/science/biology/blast {
inherit (darwin.apple_sdk.frameworks) ApplicationServices;
};
cd-hit = callPackage ../applications/science/biology/cd-hit { };
cmtk = callPackage ../applications/science/biology/cmtk { };